GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ketodeoxyribonate-cleavage in Pseudomonas fluorescens FW300-N2E2

Align 2-deoxy-3-keto-D-ribonoate cleavage enzyme (characterized)
to candidate Pf6N2E2_4692 FIG004891: hypothetical protein in carnitine cluster

Query= reanno::WCS417:GFF1426
         (310 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4692 FIG004891:
           hypothetical protein in carnitine cluster
          Length = 295

 Score =  179 bits (455), Expect = 5e-50
 Identities = 117/321 (36%), Positives = 165/321 (51%), Gaps = 47/321 (14%)

Query: 4   NRPVIITCAVTGAIHTPSMSPHLPITAQEIADAAIGAAEAGAAIVHLHARDPNDGRPSQD 63
           N  VIITCA+TGA  T + SPH+P+T ++IADAAI AA+AGA +VH H RDP  G+ S+D
Sbjct: 2   NHDVIITCALTGAGDTTAKSPHVPVTPKQIADAAIEAAKAGATVVHCHVRDPQTGKFSRD 61

Query: 64  PALFAEFLPQIKAAS-DVVINITTG------------------GAPTMGVEERLQPVMQF 104
            AL+ E + +I+ A  D+++N+T G                      +G   RL  V + 
Sbjct: 62  VALYREVMERIREADVDIIVNLTAGMGGDLEIGAGEQPMEFGPNTDLVGPLTRLAHVEEL 121

Query: 105 KPELASLNMGSMNFGLYEMLNRFTDFKHDWERPYLEESDDRIFRNTFRDITHILNACAEN 164
            PE+ +L+ G++NFG                        D I+ +T   +        E 
Sbjct: 122 LPEICTLDCGTLNFG----------------------DGDTIYVSTPAQLRAGAKRITEL 159

Query: 165 RTRFEIECYDIGHLYTAAHFLERGLLKPPLFIQSVFGLRGGIGGHPEDLAHMRRTADRLF 224
             + E+E +D GHL+ A   ++ GLL  PLF Q   G+  G    P D   M+   D L 
Sbjct: 160 GVKAELEIFDTGHLWFAKQLIKEGLLDNPLF-QLCLGIPWGA---PADTTTMKAMVDNL- 214

Query: 225 GSDYVWSILGAGRGQIPLATMGLSMGSNARVGLEDSLWDGPGKLAASNADQVRRIRTVIE 284
            +D VW+  G GR Q+P+A   + +G N RVGLED+LW   G L A+N   V R   ++ 
Sbjct: 215 PADAVWAGFGIGRMQMPMAAQAVLLGGNVRVGLEDNLWLDKGVL-ATNGQLVERAGEILS 273

Query: 285 ALGHRVATPDEAREILGLKGR 305
            LG RV TP E R+ +GL  R
Sbjct: 274 RLGARVLTPAEGRKKMGLTQR 294


Lambda     K      H
   0.321    0.138    0.416 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 239
Number of extensions: 12
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 310
Length of database: 295
Length adjustment: 27
Effective length of query: 283
Effective length of database: 268
Effective search space:    75844
Effective search space used:    75844
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory